| With the discovery of small regulatory RNAs, there has been a tremendous increase in the number of RNA sequencing projects. Meanwhile, novel high-throughput sequencing technologies, which can sequence as much as 500,000 small RNA sequences in one run, have emerged. The challenge of processing this rapidly growing data can be addressed by optimizing current analysis approaches for small RNA sequences.;Keywords: sequence analysis; global alignment; genome mapping; register-level programming; small RNAs;We present fast register-level methods for small RNA pairwise alignment and small RNA to genome mapping. Both methods are parallelized for further efficiency. We employ these methods for: (1) evaluation of the correlation between evolutionary distance of small RNAs and physical distance of their genomic targets and (2) reducing redundancy in a given set of small RNAs by filtering sequence and genomic target overlaps. We test our methods on small RNA sequences from O.sativa, P.contorta, and Mus musculus. |
